Plot the disambiguated counts per cell.
Usage
plotCountsPerCell(object, ...)
# S4 method for class 'SingleCellExperiment'
plotCountsPerCell(
object,
geom = c("histogram", "ecdf", "violin", "ridgeline", "boxplot"),
interestingGroups = NULL,
min = 0L,
max = Inf,
point = c("none", "inflection", "knee"),
trans = "log10",
title = "Counts per cell"
)
Arguments
- object
Object.
- geom
character(1)
. Plot type. Usesmatch.arg()
internally and defaults to the first argument in thecharacter
vector.- interestingGroups
character
. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.- min
numeric(1)
. Recommended minimum value cutoff.- max
numeric(1)
. Recommended maximum value cutoff.- point
character(1)
. Label either the knee or inflection points per sample. Requiresgeom = "ecdf"
.- trans
character(1)
. Name of the axis scale transformation to apply.For more information:
- title
character(1)
. Title.- ...
Additional arguments.
Details
"Counts" refer to universal molecular identifier (UMI) counts for droplet-based scRNA-seq data.
Examples
data(SingleCellExperiment_splatter, package = "AcidTest")
## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
plotCountsPerCell(object, geom = "violin")
plotCountsPerCell(object, geom = "ridgeline")
#> Picking joint bandwidth of 0.0318
plotCountsPerCell(object, geom = "ecdf")
plotCountsPerCell(object, geom = "histogram")
plotCountsPerCell(object, geom = "boxplot")